Related papers: Fast and Lightweight Distributed Suffix Array Cons…
The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
We first describe three algorithms for computing the Lyndon array that have been suggested in the literature, but for which no structured exposition has been given. Two of these algorithms execute in quadratic time in the worst case, the…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
We present a simple algorithm for computing the document array given a string collection and its suffix array as input. Our algorithm runs in linear time using constant additional space for strings from constant alphabets.
A keyword dictionary is an associative array whose keys are strings. Recent applications handling massive keyword dictionaries in main memory have a need for a space-efficient implementation. When limited to static applications, there are a…
Current efficient fine-tuning methods (e.g., adapters, prefix-tuning, etc.) have optimized conditional text generation via training a small set of extra parameters of the neural language model, while freezing the rest for efficiency. While…
We introduce an extension of the XQuery language, FluX, that supports event-based query processing and the conscious handling of main memory buffers. Purely event-based queries of this language can be executed on streaming XML data in a…
We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
Modern large-scale deep learning workloads highlight the need for parallel execution across many devices in order to fit model data into hardware accelerator memories. In these settings, array redistribution may be required during a…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
Suffix trees and suffix arrays are two of the most widely used data structures for text indexing. Each uses linear space and can be constructed in linear time for polynomially sized alphabets. However, when it comes to answering queries…
Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…
Cuckoo hashing [4] is a multiple choice hashing scheme in which each item can be placed in multiple locations, and collisions are resolved by moving items to their alternative locations. In the classical implementation of two-way cuckoo…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
XML document markup is highly repetitive and therefore well compressible using dictionary-based methods such as DAGs or grammars. In the context of selectivity estimation, grammar-compressed trees were used before as synopsis for structural…
Arising from: Mankowitz, D.J., Michi, A., Zhernov, A. et al. Faster sorting algorithms discovered using deep reinforcement learning.Nature 618, 257-263 (2023). doi.org/10.1038/s41586-023-06004-9. The article cited above presents new…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…